Flames of Vengeance retroactively applies many changes which are introduced in DKS also to Ego Draconis. Most engine changes for instance are immediately present in Ego Draconis. To maintain compatibility with existing savegames however, there are a number of things which aren't changed when you install FOV. These are:

Enemy placement and balancing (massive overhaul)Loot and set-items (complete overhaul)Story and scripting changes (e.g. in DKS flying fortress gameplay is very different to ED)Art changes in Ego Draconis (though you do get the advantage of better lighting & shading)

In general, if you played or finished Ego Draconis and don't want to start over again, get FOV.

If you don't mind starting over again, get DKS, in which the total gameplay experience is in my opinion much more stream-lined.

There's no big differences between the FOV content in DKS and the FOV content applied to ED.